OP, how would you have felt if the conversation had gone the other way and your friend had said that, when her dc grow up, she's keeping her fingers crossed that they don't get married to Catholics because she doesn't want to think that she would have grandchildren that are forced to believe in some imaginary friend because of the partner, how can an educated person believe that there is some god figure out there controlling our lives, it's ridiculous... [or insert any other belief that an atheist might have about Catholic beliefs - I'm not saying I agree with it, just putting it here for the sake of the discussion]
If you think that if your friend said the above to you and you thought it was an offensive comment about your beliefs and thoughts and that it shows that they think you are not as good as them, then that is exactly what your friend thought you were saying about her and her family, albeit with the belief systems reversed. And that is why she found what you were saying so hurtful.
Because although you did say that it would be ok for your dd to marry someone who was not catholic, you would prefer her to find a catholic. Assuming she had a son who was of the right age and who your dd liked enough to get married, you'd be thinking 'great, but if only he was catholic he would be perfect...' and therefore again you are saying that you think your dd could have done better.
Maybe she is sitting at home thinking 'this is a women who is well educated and has sense well i thought she had sense' about your beliefs too - would that surprise or hurt you if you thought that that's the reaction your comments caused about you?
I can see that you probably didn't mean to be insulting when you made the comment, but it is a bit worrying that you believe it so much to the exclusion of all else that you don't seem to see that, even if unintended, the comment did have the scope to be offensive if said to someone who wasn't catholic. So other people didn't react to what you said - maybe they don't like discussing religious things, or thought something but didn't say it. There's no reason to be disappointed in her - it's her beliefs and surely they are just as valid as yours. If anything your reaction to this could suggest that her reaction is making you insecure in your beliefs...
I'm cultural CofE by background, relatively little religious background from home although some strong stuff at school that they tried to indoctrinate us into. DH is Catholic. However we married in a CofE church, and have also had christened our dc as CofE. That was my choice - despite apparently there supposedly is something that says if you are catholic you are supposed to get married in a catholic church and promise to bring your dc up as catholics, even if your partner is not catholic, I actively didn't want to bring my dc up as catholic. Of DH and many other friends I have that are catholic very few of them have actively searched out a catholic partner, even fewer of them have ended up with a catholic partner and like me, none of them have gone down the bringing up the kids as catholics route.
I'm not really sure why I'm putting this here - just that if I had had parents (or if dh had or any of our catholic friends) that were so into their religion that they would actively like us to pick a partner who was of the same religion (whether implicitly or explicitly) then lots of good marriages would never have happened which would have been a real shame.